The obvious reason to compare these two trees is for their use in biodiesel production which both of them are currently used for. I have divided this answer into the particular components of the question and then determined whether Jatropha was better, Pongomia was better or it was a tie.
Carbon Sequestration-Tie or Jatropha
At full growth Pongamia trees have a 10-meter taproot which makes it a carbon sink. It sequesters more than 50 tonnes of Co2 per hectare per year. Jatropha forests also create carbon sinks. But both plants are burned as biofuels meaning that they produce Co2 at that time. The Jatropha plant recycles that Co2 and is considered carbon “neutral” because of this. I do not have data suggesting whether Pongamia trees are also totally neutral or if they sequester more Co2 than they put out.
The Pongamia tree is highly resilient to drought and other intense climates which makes it able to be grown in land that would otherwise wouldn’t be able to grow plantlife. This means that it improves the soil as it needs to essentially “fix” the soil so that it can get the water and nutrients from it. The Jatropha plant has also been shown to improve soil and also does well in harsh climates.
They are also low-maintenance plants meaning less workers are needed. One worker can cover 15 hectares of Jatropha plants while one worker working with Pongamia plants can cover 60 hectares. Jatropha plants are fairly labor intensive and thus require more maintenance.
In a year Pongamia produces just a few more tonnes per hectare as Jatropha but over a 6 year period of time will produce twice as much as Jatropha. Jatropha is also labor intensive meaning that more workers (and thus more money) are needed to produce a plant which produces at only half the rate of Pongamia. In this aspect Pongamia is obviously much more economical.
Based on these answers it seems the Pongomia tree is a better biofuel source than Jatropha based on the questions asked.
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